no real overall trends
#### clonality
Because why not
this data is already log10(inv.simp)
## [[1]]
##
## [[2]]
##
## [[3]]
##
## [[4]]
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## [[5]]
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## [[7]]
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## 1-1 1-3 10-1 10-3 10-5 11-1 11-3 11-5 12-1 12-3 12-5 13-1 13-5 14-1 14-5 15-1
## 469 372 53 104 79 144 134 212 122 353 565 74 88 402 407 73
## 15-5 16-1 16-5 17-1 17-5 18-1 18-5 19-1 19-5 2-1 2-3 2-5 20-1 20-5 21-1 22-5
## 77 86 79 236 271 198 373 82 80 180 143 145 138 9 28 53
## 23-1 23-5 24-1 24-5 3-1 3-3 3-5 5-1 5-3 5-5 6-1 6-3 6-5 7-1 7-3 7-5
## 1 84 255 245 28 21 28 91 270 377 327 286 124 35 45 18
## 8-1 8-3 8-5 9-1 9-3 9-5
## 23 14 9 210 52 127
this data is already log10(inv.simp)
## [[1]]
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## [[9]]
#### clonotype size rarefaction
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the pre-post tils always strong cluster in overlap/jaccard/morisita 26/9/3/12 consistent, 19 and 7 iffy (7 really low counts)
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morisita looks beautiful, all patients cluster really strongly some mixing with the low 20’s in jaccard and overlap, but overall very strong
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overlap is nearly perfect (just 3til and 3pbmc separate but still have an island of overlap out there), jaccard good but mixes some up, morisita segregates like all the til from nontil
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yo jaccard ignores proportions/clones, just based off cdr3s
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looks like generally stronger 5-7 overlap (but small and not much for any other)
the questionable data shows enrichment towards both extremes with outliers removed though, it looks like just increase in TM overlap for NLR
it kinda looked like something was there, but looks inconclusive
this is erroring right now for me? 08.19 don’t have scaling worked out yet, and this is overall but treg lot of overlap cd4act cd8, cd8exh-act strong, cd4 act-exh?
not much clinical diff, maybe a bit more single in nr more 2+ in nr, more 2 in nlr/maybe l; the high nr outliers are 17
## [[1]]
## [[1]]$`CD8 TEMRA`
## [1] 78
##
## [[1]]$Other
## [1] 1927
##
##
## [[2]]
## [[2]]$`CD8 TEMRA`
## [1] 57
##
## [[2]]$Other
## [1] 1804
##
##
## [[3]]
## [[3]]$`CD8 TEMRA`
## [1] 11
##
## [[3]]$Other
## [1] 1351
##
##
## [[4]]
## [[4]]$`CD8 TEMRA`
## [1] 51
##
## [[4]]$Other
## [1] 2086
##
##
## [[5]]
## [[5]]$`CD8 TEMRA`
## [1] 36
##
## [[5]]$Other
## [1] 2477
##
##
## [[6]]
## [[6]]$`CD8 TEMRA`
## [1] 57
##
## [[6]]$Other
## [1] 2428
##
##
## [[7]]
## [[7]]$`CD8 TEMRA`
## [1] 85
##
## [[7]]$Other
## [1] 1682
##
##
## [[8]]
## [[8]]$`CD8 TEMRA`
## [1] 128
##
## [[8]]$Other
## [1] 3636
##
##
## [[9]]
## [[9]]$`CD8 TEMRA`
## [1] 15
##
## [[9]]$Other
## [1] 1407
##
##
## [[10]]
## [[10]]$`CD8 TEMRA`
## [1] 41
##
## [[10]]$Other
## [1] 3290
##
##
## [[11]]
## [[11]]$`CD8 TEMRA`
## [1] 75
##
## [[11]]$Other
## [1] 6180
##
##
## [[12]]
## [[12]]$`CD8 TEMRA`
## [1] 43
##
## [[12]]$Other
## [1] 1737
##
##
## [[13]]
## [[13]]$`CD8 TEMRA`
## [1] 68
##
## [[13]]$Other
## [1] 2179
##
##
## [[14]]
## [[14]]$`CD8 TEMRA`
## [1] 170
##
## [[14]]$Other
## [1] 1055
##
##
## [[15]]
## [[15]]$`CD8 TEMRA`
## [1] 134
##
## [[15]]$Other
## [1] 1315
##
##
## [[16]]
## [[16]]$`CD8 TEMRA`
## [1] 50
##
## [[16]]$Other
## [1] 2639
##
##
## [[17]]
## [[17]]$`CD8 TEMRA`
## [1] 41
##
## [[17]]$Other
## [1] 2943
##
##
## [[18]]
## [[18]]$`CD8 TEMRA`
## [1] 55
##
## [[18]]$Other
## [1] 1981
##
##
## [[19]]
## [[19]]$`CD8 TEMRA`
## [1] 57
##
## [[19]]$Other
## [1] 1957
##
##
## [[20]]
## [[20]]$`CD8 TEMRA`
## [1] 197
##
## [[20]]$Other
## [1] 799
##
##
## [[21]]
## [[21]]$`CD8 TEMRA`
## [1] 189
##
## [[21]]$Other
## [1] 975
##
##
## [[22]]
## [[22]]$`CD8 TEMRA`
## [1] 42
##
## [[22]]$Other
## [1] 466
##
##
## [[23]]
## [[23]]$`CD8 TEMRA`
## [1] 58
##
## [[23]]$Other
## [1] 932
##
##
## [[24]]
## [[24]]$`CD8 TEMRA`
## [1] 94
##
## [[24]]$Other
## [1] 1702
##
##
## [[25]]
## [[25]]$`CD8 TEMRA`
## [1] 89
##
## [[25]]$Other
## [1] 2732
##
##
## [[26]]
## [[26]]$`CD8 TEMRA`
## [1] 125
##
## [[26]]$Other
## [1] 2323
##
##
## [[27]]
## [[27]]$`CD8 TEMRA`
## [1] 90
##
## [[27]]$Other
## [1] 2416
##
##
## [[28]]
## [[28]]$`CD8 TEMRA`
## [1] 104
##
## [[28]]$Other
## [1] 1876
##
##
## [[29]]
## [[29]]$`CD8 TEMRA`
## [1] 96
##
## [[29]]$Other
## [1] 1530
##
##
## [[30]]
## [[30]]$`CD8 TEMRA`
## [1] 28
##
## [[30]]$Other
## [1] 60
##
##
## [[31]]
## [[31]]$`CD8 TEMRA`
## [1] 77
##
## [[31]]$Other
## [1] 2664
##
##
## [[32]]
## [[32]]$`CD8 TEMRA`
## [1] 70
##
## [[32]]$Other
## [1] 2951
##
##
## [[33]]
## [[33]]$`CD8 TEMRA`
## [1] 62
##
## [[33]]$Other
## [1] 3290
##
##
## [[34]]
## [[34]]$`CD8 TEMRA`
## [1] 62
##
## [[34]]$Other
## [1] 2710
##
##
## [[35]]
## [[35]]$`CD8 TEMRA`
## [1] 75
##
## [[35]]$Other
## [1] 1792
##
##
## [[36]]
## [[36]]$`CD8 TEMRA`
## [1] 163
##
## [[36]]$Other
## [1] 1184
##
##
## [[37]]
## [[37]]$`CD8 TEMRA`
## [1] 117
##
## [[37]]$Other
## [1] 1538
##
##
## [[38]]
## [[38]]$`CD8 TEMRA`
## [1] 25
##
## [[38]]$Other
## [1] 377
##
##
## [[39]]
## [[39]]$`CD8 TEMRA`
## [1] 85
##
## [[39]]$Other
## [1] 2003
##
##
## [[40]]
## [[40]]$`CD8 TEMRA`
## [1] 109
##
## [[40]]$Other
## [1] 4644
##
##
## [[41]]
## [[41]]$`CD8 TEMRA`
## [1] 111
##
## [[41]]$Other
## [1] 2593
##
##
## [[42]]
## [[42]]$`CD8 TEMRA`
## [1] 95
##
## [[42]]$Other
## [1] 2792
##
##
## [[43]]
## [[43]]$`CD8 TEMRA`
## [1] 73
##
## [[43]]$Other
## [1] 1113
##
##
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## [[44]]$`CD8 TEMRA`
## [1] 110
##
## [[44]]$Other
## [1] 1797
##
##
## [[45]]
## [[45]]$`CD8 TEMRA`
## [1] 101
##
## [[45]]$Other
## [1] 2186
##
##
## [[46]]
## [[46]]$`CD8 TEMRA`
## [1] 48
##
## [[46]]$Other
## [1] 517
##
##
## [[47]]
## [[47]]$`CD8 TEMRA`
## [1] 68
##
## [[47]]$Other
## [1] 2155
##
##
## [[48]]
## [[48]]$`CD8 TEMRA`
## [1] 219
##
## [[48]]$Other
## [1] 1542
##
##
## [[49]]
## [[49]]$`CD8 TEMRA`
## [1] 90
##
## [[49]]$Other
## [1] 1667
##
##
## [[50]]
## [[50]]$`CD8 TEMRA`
## [1] 63
##
## [[50]]$Other
## [1] 2002
##
##
## [[51]]
## [[51]]$`CD8 TEMRA`
## [1] 26
##
## [[51]]$Other
## [1] 854
##
##
## [[52]]
## [[52]]$`CD8 TEMRA`
## [1] 54
##
## [[52]]$Other
## [1] 1741
##
##
## [[53]]
## named list()
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## named list()
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## [[56]]
## named list()
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## named list()
still not entirely sure about the mechanics of vegdist could still be a size effect of the temra, haven’t done downsampling also mean or median for the column version?
got some interesting ones, 25 is just 14, 15 strong 23/5, 23-1 is just 6 cells, 21-1 is 200 cells specific clusts - 3 (l high - temra right),8 (nlr lo - cd8 naive), 12 (nlr hi, cd4 activated ish, center top), 16 (nlr hi - dead?), 18(nlr hi,l lo, cd4 naive),21 (nlr hi - cd4 early?), 24 (l lo,cd8-4 transition), 29 (l lo - left gdt), ldat clusts - 4(nlr lo-cd14mono),9(nlr hi-cd16 mono),19(l lo-cdc),21(nlr hi-cd16nk.2),22(l lo-cd56 nk),26(nlr hi-pdc),28(l lo,nlr hi-mono??),29(l hi-plasma),31(l lo-progenitor),32(l lo-b/mono)
## [[1]]
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## [[2]]
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## [[3]]
Lynch has higher prop of clones TM, decreases over time
## [[1]]
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## [[2]]
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## [[3]]
lynch highest prop TM, NLR second NLR is a lot more TM porpotion increase while others decrease But none of this translates to any pattern in change in TM clonality this could also be the result of sample size of pbmc and til - manual jaccard is better?
could do proportion of TMs for each by cell type or proportional composition of TMs for clinical by cell type and then uhhh raref TMs or actually that’s more div stuff